PLUMED-NEST-TEST-SITE

Project ID: plumID:20.014
Source: PLUMED_input_files/AB42_alone/plumed/plumed.dat
Originally used with PLUMED version: 2.6.0
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

#SETTINGS NREPLICAS=2
#this is the master plumed.dat file for metadynamic metainference simulations

# define groups
MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
STRUCTURE
a file in pdb format containing a reference structure
=../system/template.pdb
The MOLINFO action with label  calculates something
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-627
FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=1000

#include file with definition of metadynamics CVs
INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
 
FILE
file to be included
=CVs.dat
# The command:
# INCLUDE FILE=CVs.dat
# ensures PLUMED loads the contents of the file called CVs.dat
# The contents of this file are shown below (click the red comment to hide them).
#This is the metadynamics CV file

#CV1 alpha helix
The INCLUDE action with label CVs.dat calculates something
ALPHARMSD
Probe the alpha helical content of a protein structure. More details
 
RESIDUES
this command is used to specify the set of residues that could conceivably form part of the secondary structure
=all 
TYPE
 the manner in which RMSD alignment is performed
=DRMSD 
LESS_THAN
calculate the number of a residue segments that are within a certain target distance of this secondary structure type
={RATIONAL R_0=0.08 NN=8 MM=12} 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=helix

#CV2 sum parallel and anti-parallel beta-content
The ALPHARMSD action with label helix calculates the following quantities:
 Quantity   
 Description  
helix.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
helix.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold
PARABETARMSD
Probe the parallel beta sheet content of your protein structure. More details
 
RESIDUES
this command is used to specify the set of residues that could conceivably form part of the secondary structure
=all 
TYPE
 the manner in which RMSD alignment is performed
=DRMSD 
LESS_THAN
calculate the number of a residue segments that are within a certain target distance of this secondary structure type
={RATIONAL R_0=0.08 NN=8 MM=12} 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=par
The PARABETARMSD action with label par calculates the following quantities:
 Quantity   
 Description  
par.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
par.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold
ANTIBETARMSD
Probe the antiparallel beta sheet content of your protein structure. More details
 
RESIDUES
this command is used to specify the set of residues that could conceivably form part of the secondary structure
=all 
TYPE
 the manner in which RMSD alignment is performed
=DRMSD 
LESS_THAN
calculate the number of a residue segments that are within a certain target distance of this secondary structure type
={RATIONAL R_0=0.08 NN=8 MM=12} 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=anti
The ANTIBETARMSD action with label anti calculates the following quantities:
 Quantity   
 Description  
anti.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
anti.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=par.lessthan,anti.lessthan 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=beta

#CV3 radius of gyration
The COMBINE action with label beta calculates the following quantities:
 Quantity   
 Description  
beta.value
a linear compbinationca: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=5,17,27,42,62,86,103,115,126,133,154,169,185,202,219,236,258,277,293,313,333,343,358,370,386,393,404,418,440,447,457,476,495,502,521,538,554,561,568,584,600,619
The GROUP action with label ca calculates somethingrgyr: 
GYRATION
Calculate the radius of gyration, or other properties related to it. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=ca 
NOPBC
 ignore the periodic boundary conditions when calculating distances

#CV4 contacts between hydrophobic residues calculated as the number of Cbeta carbon couples closer than 0.6 nm 
The GYRATION action with label rgyr calculates the following quantities:
 Quantity   
 Description  
rgyr.value
the radius that was computed from the weights
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=19,44,171,260,279,295,315,335,372,449,459,478,504,523,540,570,586,602,621 
R_0
The r_0 parameter of the switching function
=0.6 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.0 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hydro

#CV5 the number of salt-bridges calculated as the number of couples of heavy atoms from the charged group closer than 0.6 nm 
#GROUP A is all the heavy atoms from RCOO- group of aspartic acids and glutamic acids 
#GROUP B is all the heavy atoms from RHN3+ from lysines or (RNHC(NH2)2+) of arginines
The COORDINATION action with label hydro calculates the following quantities:
 Quantity   
 Description  
hydro.value
the value of the coordination
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=10,11,12,35,36,37,108,109,110,162,163,164,351,352,353,363,364,365 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=75,76,77,78,79,80,81,250,251,252,253,432,433,434,435 
R_0
The r_0 parameter of the switching function
=0.6 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.0 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=salt

#CV6 correlation between consecutive psi torsion angles.
The COORDINATION action with label salt calculates the following quantities:
 Quantity   
 Description  
salt.value
the value of the coordination
DIHCOR
Measures the degree of similarity between dihedral angles. More details
 ...
ATOMS1
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-1
the four atoms that are required to calculate the psi dihedral for residue 1. Click here for more information. 
,
@psi-2
the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
ATOMS2
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-2
the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
,
@psi-3
the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. 
ATOMS3
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-3
the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. 
,
@psi-4
the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. 
ATOMS4
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-4
the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. 
,
@psi-5
the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. 
ATOMS5
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-5
the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. 
,
@psi-6
the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information. 
ATOMS6
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-6
the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information. 
,
@psi-7
the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. 
ATOMS7
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-7
the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. 
,
@psi-8
the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. 
ATOMS8
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-8
the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. 
,
@psi-9
the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information. 
ATOMS9
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-9
the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information. 
,
@psi-10
the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information. 
ATOMS10
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-10
the four atoms that are required to calculate the psi dihedral for residue 10. Click here for more information. 
,
@psi-11
the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information. 
ATOMS11
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-11
the four atoms that are required to calculate the psi dihedral for residue 11. Click here for more information. 
,
@psi-12
the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information. 
ATOMS12
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-12
the four atoms that are required to calculate the psi dihedral for residue 12. Click here for more information. 
,
@psi-13
the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information. 
ATOMS13
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-13
the four atoms that are required to calculate the psi dihedral for residue 13. Click here for more information. 
,
@psi-14
the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information. 
ATOMS14
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-14
the four atoms that are required to calculate the psi dihedral for residue 14. Click here for more information. 
,
@psi-15
the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information. 
ATOMS15
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-15
the four atoms that are required to calculate the psi dihedral for residue 15. Click here for more information. 
,
@psi-16
the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information. 
ATOMS16
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-16
the four atoms that are required to calculate the psi dihedral for residue 16. Click here for more information. 
,
@psi-17
the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information. 
ATOMS17
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-17
the four atoms that are required to calculate the psi dihedral for residue 17. Click here for more information. 
,
@psi-18
the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information. 
ATOMS18
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-18
the four atoms that are required to calculate the psi dihedral for residue 18. Click here for more information. 
,
@psi-19
the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information. 
ATOMS19
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-19
the four atoms that are required to calculate the psi dihedral for residue 19. Click here for more information. 
,
@psi-20
the four atoms that are required to calculate the psi dihedral for residue 20. Click here for more information. 
ATOMS20
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-20
the four atoms that are required to calculate the psi dihedral for residue 20. Click here for more information. 
,
@psi-21
the four atoms that are required to calculate the psi dihedral for residue 21. Click here for more information. 
ATOMS21
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-21
the four atoms that are required to calculate the psi dihedral for residue 21. Click here for more information. 
,
@psi-22
the four atoms that are required to calculate the psi dihedral for residue 22. Click here for more information. 
ATOMS22
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-22
the four atoms that are required to calculate the psi dihedral for residue 22. Click here for more information. 
,
@psi-23
the four atoms that are required to calculate the psi dihedral for residue 23. Click here for more information. 
ATOMS23
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-23
the four atoms that are required to calculate the psi dihedral for residue 23. Click here for more information. 
,
@psi-24
the four atoms that are required to calculate the psi dihedral for residue 24. Click here for more information. 
ATOMS24
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-24
the four atoms that are required to calculate the psi dihedral for residue 24. Click here for more information. 
,
@psi-25
the four atoms that are required to calculate the psi dihedral for residue 25. Click here for more information. 
ATOMS25
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-25
the four atoms that are required to calculate the psi dihedral for residue 25. Click here for more information. 
,
@psi-26
the four atoms that are required to calculate the psi dihedral for residue 26. Click here for more information. 
ATOMS26
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-26
the four atoms that are required to calculate the psi dihedral for residue 26. Click here for more information. 
,
@psi-27
the four atoms that are required to calculate the psi dihedral for residue 27. Click here for more information. 
ATOMS27
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-27
the four atoms that are required to calculate the psi dihedral for residue 27. Click here for more information. 
,
@psi-28
the four atoms that are required to calculate the psi dihedral for residue 28. Click here for more information. 
ATOMS28
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-28
the four atoms that are required to calculate the psi dihedral for residue 28. Click here for more information. 
,
@psi-29
the four atoms that are required to calculate the psi dihedral for residue 29. Click here for more information. 
ATOMS29
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-29
the four atoms that are required to calculate the psi dihedral for residue 29. Click here for more information. 
,
@psi-30
the four atoms that are required to calculate the psi dihedral for residue 30. Click here for more information. 
ATOMS30
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-30
the four atoms that are required to calculate the psi dihedral for residue 30. Click here for more information. 
,
@psi-31
the four atoms that are required to calculate the psi dihedral for residue 31. Click here for more information. 
ATOMS31
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-31
the four atoms that are required to calculate the psi dihedral for residue 31. Click here for more information. 
,
@psi-32
the four atoms that are required to calculate the psi dihedral for residue 32. Click here for more information. 
ATOMS32
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-32
the four atoms that are required to calculate the psi dihedral for residue 32. Click here for more information. 
,
@psi-33
the four atoms that are required to calculate the psi dihedral for residue 33. Click here for more information. 
ATOMS33
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-33
the four atoms that are required to calculate the psi dihedral for residue 33. Click here for more information. 
,
@psi-34
the four atoms that are required to calculate the psi dihedral for residue 34. Click here for more information. 
ATOMS34
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-34
the four atoms that are required to calculate the psi dihedral for residue 34. Click here for more information. 
,
@psi-35
the four atoms that are required to calculate the psi dihedral for residue 35. Click here for more information. 
ATOMS35
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-35
the four atoms that are required to calculate the psi dihedral for residue 35. Click here for more information. 
,
@psi-36
the four atoms that are required to calculate the psi dihedral for residue 36. Click here for more information. 
ATOMS36
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-36
the four atoms that are required to calculate the psi dihedral for residue 36. Click here for more information. 
,
@psi-37
the four atoms that are required to calculate the psi dihedral for residue 37. Click here for more information. 
ATOMS37
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-37
the four atoms that are required to calculate the psi dihedral for residue 37. Click here for more information. 
,
@psi-38
the four atoms that are required to calculate the psi dihedral for residue 38. Click here for more information. 
ATOMS38
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-38
the four atoms that are required to calculate the psi dihedral for residue 38. Click here for more information. 
,
@psi-39
the four atoms that are required to calculate the psi dihedral for residue 39. Click here for more information. 
ATOMS39
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-39
the four atoms that are required to calculate the psi dihedral for residue 39. Click here for more information. 
,
@psi-40
the four atoms that are required to calculate the psi dihedral for residue 40. Click here for more information. 
ATOMS40
the set of 8 atoms that are being used each of the dihedral correlation values
=
@psi-40
the four atoms that are required to calculate the psi dihedral for residue 40. Click here for more information. 
,
@psi-41
the four atoms that are required to calculate the psi dihedral for residue 41. Click here for more information. 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=dihcor
NOPBC
 ignore the periodic boundary conditions when calculating distances
... DIHCOR

# --- End of included input --- 
# Chemical shifts at 278 K
The DIHCOR action with label dihcor calculates the following quantities:
 Quantity   
 Description  
dihcor.value
the sum of all the dihedral correlationscs: 
CS2BACKBONE
Calculates the backbone chemical shifts for a protein. More details
 
ATOMS
The atoms to be included in the calculation, e
=1-627 
DATADIR
 The folder with the experimental chemical shifts
=../data 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
TEMPLATE
 A PDB file of the protein system
=../system/template.pdb

#activate parallel bias metadynamics 
The CS2BACKBONE action with label cs calculates the following quantities:
 Quantity   
 Description  
cs.score
the Metainference score
cs.sigma
uncertainty parameter
cs.sigmaMean
uncertainty in the mean estimate
cs.neff
effective number of replicas
cs.acceptSigma
MC acceptance for sigma values
cs.ha
the calculated Ha hydrogen chemical shifts
cs.hn
the calculated H hydrogen chemical shifts
cs.nh
the calculated N nitrogen chemical shifts
cs.ca
the calculated Ca carbon chemical shifts
cs.cb
the calculated Cb carbon chemical shifts
cs.co
the calculated C' carbon chemical shifts
cs.expha
the experimental Ha hydrogen chemical shifts
cs.exphn
the experimental H hydrogen chemical shifts
cs.expnh
the experimental N nitrogen chemical shifts
cs.expca
the experimental Ca carbon chemical shifts
cs.expcb
the experimental Cb carbon chemical shifts
cs.expco
the experimental C' carbon chemical shifts
cs.value
the backbone chemical shifts
PBMETAD
Used to performed Parallel Bias metadynamics. More details
 ...
    
ARG
the input for this action is the scalar output from one or more other actions
=helix.lessthan,beta,rgyr,hydro,salt,dihcor
    
HEIGHT
the height of the Gaussian hills, one for all biases
=1.2
    
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases
=24 #10*SQRT(NUM_OF_CVS)
    
SIGMA
the widths of the Gaussian hills
=0.64,0.33,0.03,0.69,2.75,1.34
    
PACE
the frequency for hill addition, one for all biases
=500
    
GRID_MIN
the lower bounds for the grid
=-1,-1,-1,-1,-1,-1
    
GRID_MAX
the upper bounds for the grid
=100,100,20,200,400,50
    
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.1,0.1,0.01,0.1,0.1,0.01    
    
GRID_WSTRIDE
frequency for dumping the grid
=10000
#    GRID_RFILES=GRID.helix.lessthan,GRID.beta,GRID.rgyr,GRID.hydro,GRID.salt,GRID.dihcor
    
FILE
files in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found
=HILLS_helix,HILLS_beta,HILLS_rgyr,HILLS_hydro,HILLS_salt,HILLS_dihcor
    
WALKERS_MPI
 Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=pbmetad
... PBMETAD

# Metainference - one sigma per nucleus
The PBMETAD action with label pbmetad calculates the following quantities:
 Quantity   
 Description  
pbmetad.bias
the instantaneous value of the bias potentialcs_ha: 
METAINFERENCE
Calculates the Metainference energy for a set of experimental data. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=(cs\.ha-.*),pbmetad.bias 
PARARG
reference values for the experimental data, these can be provided as arguments without derivatives
=(cs\.expha 
SIGMA0
 initial value of the uncertainty parameter
=9.0 
SIGMA_MIN
 minimum value of the uncertainty parameter
=0.00001 
SIGMA_MAX
 maximum value of the uncertainty parameter
=10.0 
DSIGMA
maximum MC move of the uncertainty parameter
=0.1 
NOISETYPE
 functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=GAUSS 
REWEIGHT
 simple REWEIGHT using the latest ARG as energy
 
SIGMA_MEAN0
starting value for the uncertainty in the mean estimate
=0.5 
OPTSIGMAMEAN
 Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
=SEM 
AVERAGING
Stride for calculation of averaged weights and sigma_mean
=500 
WRITE_STRIDE
 write the status to a file every N steps, this can be used for restart/continuation
=2500 
STATUS_FILE
write a file with all the data useful for restart/continuation of Metainference
=MISTATUS.cs_ha
The METAINFERENCE action with label cs_ha calculates the following quantities:
 Quantity   
 Description  
cs_ha.bias
the instantaneous value of the bias potential
cs_ha.sigma
uncertainty parameter
cs_ha.sigmaMean
uncertainty in the mean estimate
cs_ha.neff
effective number of replicas
cs_ha.acceptSigma
MC acceptance for sigma values
cs_ha.weight
weights of the weighted average
cs_ha.biasDer
derivatives with respect to the biascs_hn: 
METAINFERENCE
Calculates the Metainference energy for a set of experimental data. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=(cs\.hn-.*),pbmetad.bias 
PARARG
reference values for the experimental data, these can be provided as arguments without derivatives
=(cs\.exphn 
SIGMA0
 initial value of the uncertainty parameter
=9.0 
SIGMA_MIN
 minimum value of the uncertainty parameter
=0.00001 
SIGMA_MAX
 maximum value of the uncertainty parameter
=10.0 
DSIGMA
maximum MC move of the uncertainty parameter
=0.1 
NOISETYPE
 functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=GAUSS 
REWEIGHT
 simple REWEIGHT using the latest ARG as energy
 
SIGMA_MEAN0
starting value for the uncertainty in the mean estimate
=0.5 
OPTSIGMAMEAN
 Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
=SEM 
AVERAGING
Stride for calculation of averaged weights and sigma_mean
=500 
WRITE_STRIDE
 write the status to a file every N steps, this can be used for restart/continuation
=2500 
STATUS_FILE
write a file with all the data useful for restart/continuation of Metainference
=MISTATUS.cs_hn
The METAINFERENCE action with label cs_hn calculates the following quantities:
 Quantity   
 Description  
cs_hn.bias
the instantaneous value of the bias potential
cs_hn.sigma
uncertainty parameter
cs_hn.sigmaMean
uncertainty in the mean estimate
cs_hn.neff
effective number of replicas
cs_hn.acceptSigma
MC acceptance for sigma values
cs_hn.weight
weights of the weighted average
cs_hn.biasDer
derivatives with respect to the biascs_nh: 
METAINFERENCE
Calculates the Metainference energy for a set of experimental data. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=(cs\.nh-.*),pbmetad.bias 
PARARG
reference values for the experimental data, these can be provided as arguments without derivatives
=(cs\.expnh 
SIGMA0
 initial value of the uncertainty parameter
=9.0 
SIGMA_MIN
 minimum value of the uncertainty parameter
=0.00001 
SIGMA_MAX
 maximum value of the uncertainty parameter
=10.0 
DSIGMA
maximum MC move of the uncertainty parameter
=0.1 
NOISETYPE
 functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=GAUSS 
REWEIGHT
 simple REWEIGHT using the latest ARG as energy
 
SIGMA_MEAN0
starting value for the uncertainty in the mean estimate
=0.5 
OPTSIGMAMEAN
 Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
=SEM 
AVERAGING
Stride for calculation of averaged weights and sigma_mean
=500 
WRITE_STRIDE
 write the status to a file every N steps, this can be used for restart/continuation
=2500 
STATUS_FILE
write a file with all the data useful for restart/continuation of Metainference
=MISTATUS.cs_nh
The METAINFERENCE action with label cs_nh calculates the following quantities:
 Quantity   
 Description  
cs_nh.bias
the instantaneous value of the bias potential
cs_nh.sigma
uncertainty parameter
cs_nh.sigmaMean
uncertainty in the mean estimate
cs_nh.neff
effective number of replicas
cs_nh.acceptSigma
MC acceptance for sigma values
cs_nh.weight
weights of the weighted average
cs_nh.biasDer
derivatives with respect to the biascs_ca: 
METAINFERENCE
Calculates the Metainference energy for a set of experimental data. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=(cs\.ca-.*),pbmetad.bias 
PARARG
reference values for the experimental data, these can be provided as arguments without derivatives
=(cs\.expca 
SIGMA0
 initial value of the uncertainty parameter
=9.0 
SIGMA_MIN
 minimum value of the uncertainty parameter
=0.00001 
SIGMA_MAX
 maximum value of the uncertainty parameter
=10.0 
DSIGMA
maximum MC move of the uncertainty parameter
=0.1 
NOISETYPE
 functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=GAUSS 
REWEIGHT
 simple REWEIGHT using the latest ARG as energy
 
SIGMA_MEAN0
starting value for the uncertainty in the mean estimate
=0.5 
OPTSIGMAMEAN
 Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
=SEM 
AVERAGING
Stride for calculation of averaged weights and sigma_mean
=500 
WRITE_STRIDE
 write the status to a file every N steps, this can be used for restart/continuation
=2500 
STATUS_FILE
write a file with all the data useful for restart/continuation of Metainference
=MISTATUS.cs_ca
The METAINFERENCE action with label cs_ca calculates the following quantities:
 Quantity   
 Description  
cs_ca.bias
the instantaneous value of the bias potential
cs_ca.sigma
uncertainty parameter
cs_ca.sigmaMean
uncertainty in the mean estimate
cs_ca.neff
effective number of replicas
cs_ca.acceptSigma
MC acceptance for sigma values
cs_ca.weight
weights of the weighted average
cs_ca.biasDer
derivatives with respect to the biascs_cb: 
METAINFERENCE
Calculates the Metainference energy for a set of experimental data. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=(cs\.cb-.*),pbmetad.bias 
PARARG
reference values for the experimental data, these can be provided as arguments without derivatives
=(cs\.expcb 
SIGMA0
 initial value of the uncertainty parameter
=9.0 
SIGMA_MIN
 minimum value of the uncertainty parameter
=0.00001 
SIGMA_MAX
 maximum value of the uncertainty parameter
=10.0 
DSIGMA
maximum MC move of the uncertainty parameter
=0.1 
NOISETYPE
 functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=GAUSS 
REWEIGHT
 simple REWEIGHT using the latest ARG as energy
 
SIGMA_MEAN0
starting value for the uncertainty in the mean estimate
=0.5 
OPTSIGMAMEAN
 Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
=SEM 
AVERAGING
Stride for calculation of averaged weights and sigma_mean
=500 
WRITE_STRIDE
 write the status to a file every N steps, this can be used for restart/continuation
=2500 
STATUS_FILE
write a file with all the data useful for restart/continuation of Metainference
=MISTATUS.cs_cb
The METAINFERENCE action with label cs_cb calculates the following quantities:
 Quantity   
 Description  
cs_cb.bias
the instantaneous value of the bias potential
cs_cb.sigma
uncertainty parameter
cs_cb.sigmaMean
uncertainty in the mean estimate
cs_cb.neff
effective number of replicas
cs_cb.acceptSigma
MC acceptance for sigma values
cs_cb.weight
weights of the weighted average
cs_cb.biasDer
derivatives with respect to the biascs_co: 
METAINFERENCE
Calculates the Metainference energy for a set of experimental data. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=(cs\.co-.*),pbmetad.bias 
PARARG
reference values for the experimental data, these can be provided as arguments without derivatives
=(cs\.expco 
SIGMA0
 initial value of the uncertainty parameter
=9.0 
SIGMA_MIN
 minimum value of the uncertainty parameter
=0.00001 
SIGMA_MAX
 maximum value of the uncertainty parameter
=10.0 
DSIGMA
maximum MC move of the uncertainty parameter
=0.1 
NOISETYPE
 functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=GAUSS 
REWEIGHT
 simple REWEIGHT using the latest ARG as energy
 
SIGMA_MEAN0
starting value for the uncertainty in the mean estimate
=0.5 
OPTSIGMAMEAN
 Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
=SEM 
AVERAGING
Stride for calculation of averaged weights and sigma_mean
=500 
WRITE_STRIDE
 write the status to a file every N steps, this can be used for restart/continuation
=2500 
STATUS_FILE
write a file with all the data useful for restart/continuation of Metainference
=MISTATUS.cs_co

# Ensemble statistics
The METAINFERENCE action with label cs_co calculates the following quantities:
 Quantity   
 Description  
cs_co.bias
the instantaneous value of the bias potential
cs_co.sigma
uncertainty parameter
cs_co.sigmaMean
uncertainty in the mean estimate
cs_co.neff
effective number of replicas
cs_co.acceptSigma
MC acceptance for sigma values
cs_co.weight
weights of the weighted average
cs_co.biasDer
derivatives with respect to the biasens: 
ENSEMBLE
Calculates the replica averaging of a collective variable over multiple replicas. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=(cs\.ha-.*),(cs\.hn-.*),(cs\.nh-.*),(cs\.ca-.*),(cs\.cb-.*),(cs\.co-.*),pbmetad.bias 
REWEIGHT
 simple REWEIGHT using the latest ARG as energy

The ENSEMBLE action with label ens calculates the following quantities:
 Quantity   
 Description  
ens..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for details
STATS
Calculates statistical properties of a set of collective variables with respect to a set of reference values. More details
 ...
    
ARG
the input for this action is the scalar output from one or more other actions
=(ens\.cs\.ha-.*),(ens\.cs\.hn-.*),(ens\.cs\.nh-.*),(ens\.cs\.ca-.*),(ens\.cs\.cb-.*),(ens\.cs\.co
    
PARARG
the input for this action is the scalar output from one or more other actions without derivatives
=(cs\.expha-.*),(cs\.exphn-.*),(cs\.expnh-.*),(cs\.expca-.*),(cs\.expcb-.*),(cs\.expco 
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=stat
... STATS

#print out relevant info
The STATS action with label stat calculates the following quantities:
 Quantity   
 Description  
stat.sqdevsum
the sum of the squared deviations between arguments and parameters
stat.corr
the correlation between arguments and parameters
stat.slope
the slope of a linear fit between arguments and parameters
stat.intercept
the intercept of a linear fit between arguments and parameters
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=helix.lessthan,beta,rgyr,hydro,salt,dihcor,pbmetad.bias 
FILE
the name of the file on which to output these quantities
=COLVAR 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=(ens.*),(stat 
FILE
the name of the file on which to output these quantities
=STATS 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=(cs_ha 
FILE
the name of the file on which to output these quantities
=BAYES.HA 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=(cs_hn 
FILE
the name of the file on which to output these quantities
=BAYES.HN 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=(cs_nh 
FILE
the name of the file on which to output these quantities
=BAYES.NH 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=(cs_ca 
FILE
the name of the file on which to output these quantities
=BAYES.CA 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=(cs_cb 
FILE
the name of the file on which to output these quantities
=BAYES.CB 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=(cs_co 
FILE
the name of the file on which to output these quantities
=BAYES.CO 
STRIDE
 the frequency with which the quantities of interest should be output
=500
ENDPLUMED
Terminate plumed input. More details